How To Install freecontact on Ubuntu 22.04

In this tutorial we learn how to install freecontact on Ubuntu 22.04. freecontact is fast protein contact predictor

Introduction

In this tutorial we learn how to install freecontact on Ubuntu 22.04.

What is freecontact

freecontact is:

FreeContact is a protein residue contact predictor optimized for speed. Its input is a multiple sequence alignment. FreeContact can function as an accelerated drop-in for the published contact predictors EVfold-mfDCA of DS. Marks (2011) and PSICOV of D. Jones (2011).

FreeContact is accelerated by a combination of vector instructions, multiple threads, and faster implementation of key parts. Depending on the alignment, 8-fold or higher speedups are possible.

A sufficiently large alignment is required for meaningful results. As a minimum, an alignment with an effective (after-weighting) sequence count bigger than the length of the query sequence should be used. Alignments with tens of thousands of (effective) sequences are considered good input.

jackhmmer(1) from the hmmer package, or hhblits(1) from hhsuite can be used to generate the alignments, for example.

This package contains the command line tool freecontact(1).

There are three methods to install freecontact on Ubuntu 22.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install freecontact Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install freecontact using apt-get by running the following command:

sudo apt-get -y install freecontact

Install freecontact Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install freecontact using apt by running the following command:

sudo apt -y install freecontact

Install freecontact Using aptitude

If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install freecontact using aptitude by running the following command:

sudo aptitude -y install freecontact

How To Uninstall freecontact on Ubuntu 22.04

To uninstall only the freecontact package we can use the following command:

sudo apt-get remove freecontact

Uninstall freecontact And Its Dependencies

To uninstall freecontact and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:

sudo apt-get -y autoremove freecontact

Remove freecontact Configurations and Data

To remove freecontact configuration and data from Ubuntu 22.04 we can use the following command:

sudo apt-get -y purge freecontact

Remove freecontact configuration, data, and all of its dependencies

We can use the following command to remove freecontact configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge freecontact

References

Summary

In this tutorial we learn how to install freecontact package on Ubuntu 22.04 using different package management tools: apt, apt-get and aptitude.